Incidental Mutation 'R6135:Vps16'
ID 488277
Institutional Source Beutler Lab
Gene Symbol Vps16
Ensembl Gene ENSMUSG00000027411
Gene Name VSP16 CORVET/HOPS core subunit
Synonyms 1810074M16Rik
MMRRC Submission 044282-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.970) question?
Stock # R6135 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 130266259-130286189 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 130280573 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 200 (Y200C)
Ref Sequence ENSEMBL: ENSMUSP00000115899 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028900] [ENSMUST00000128994]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000028900
AA Change: Y200C

PolyPhen 2 Score 0.115 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000028900
Gene: ENSMUSG00000027411
AA Change: Y200C

DomainStartEndE-ValueType
Pfam:Vps16_N 4 420 1e-166 PFAM
low complexity region 452 462 N/A INTRINSIC
Pfam:Vps16_C 517 835 5.5e-150 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000125098
Predicted Effect noncoding transcript
Transcript: ENSMUST00000125973
Predicted Effect possibly damaging
Transcript: ENSMUST00000128994
AA Change: Y200C

PolyPhen 2 Score 0.569 (Sensitivity: 0.88; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000115899
Gene: ENSMUSG00000027411
AA Change: Y200C

DomainStartEndE-ValueType
Pfam:Vps16_N 4 212 3.2e-74 PFAM
Pfam:Vps16_N 205 316 1e-45 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130258
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131220
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137084
Predicted Effect noncoding transcript
Transcript: ENSMUST00000134677
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132388
Meta Mutation Damage Score 0.6048 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.2%
  • 20x: 94.7%
Validation Efficiency 100% (55/55)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human homolog of yeast class C Vps16 protein. The mammalian class C Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2009]
PHENOTYPE: Mice with a homozygous point mutation in exon 3 display impaired motor function. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 59 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2210408I21Rik A G 13: 77,402,335 (GRCm39) E95G probably damaging Het
Abca4 C T 3: 121,932,096 (GRCm39) T250I possibly damaging Het
Ahi1 G A 10: 20,845,020 (GRCm39) R375H probably benign Het
Aimp1 T C 3: 132,377,844 (GRCm39) K174E probably benign Het
Aire A G 10: 77,878,801 (GRCm39) L82P probably damaging Het
Akap13 T A 7: 75,259,656 (GRCm39) V760D possibly damaging Het
Ank3 G A 10: 69,838,395 (GRCm39) R1566K possibly damaging Het
Carf C T 1: 60,187,122 (GRCm39) S540F probably damaging Het
Ccdc171 T A 4: 83,473,087 (GRCm39) M172K probably benign Het
Chpt1 A T 10: 88,318,145 (GRCm39) V199E possibly damaging Het
Cldn16 G A 16: 26,293,018 (GRCm39) D65N possibly damaging Het
Cnga3 G A 1: 37,271,318 (GRCm39) probably benign Het
Col14a1 A G 15: 55,244,246 (GRCm39) T440A unknown Het
Creb3l3 A G 10: 80,921,552 (GRCm39) I331T probably benign Het
Cul9 T C 17: 46,832,379 (GRCm39) T1410A probably benign Het
Dnm1 T A 2: 32,223,075 (GRCm39) probably null Het
Fhl5 A T 4: 25,214,716 (GRCm39) Y20* probably null Het
Fignl1 T C 11: 11,752,557 (GRCm39) D166G probably benign Het
Ghr T C 15: 3,355,447 (GRCm39) I279V probably benign Het
Gm1979 T G 5: 26,205,298 (GRCm39) S180R probably damaging Het
Hydin T C 8: 111,189,292 (GRCm39) V1232A possibly damaging Het
Ifnar1 A G 16: 91,298,508 (GRCm39) probably null Het
Inpp5d A G 1: 87,548,119 (GRCm39) probably null Het
Itgb4 C T 11: 115,874,983 (GRCm39) R447W probably benign Het
Kcnh2 T A 5: 24,526,791 (GRCm39) S1002C probably damaging Het
Krt87 T A 15: 101,385,415 (GRCm39) E319V probably damaging Het
Lbp A G 2: 158,159,469 (GRCm39) I201V probably benign Het
Man1a2 G A 3: 100,592,248 (GRCm39) probably benign Het
Myh8 A G 11: 67,188,326 (GRCm39) T996A possibly damaging Het
Nat10 A G 2: 103,573,661 (GRCm39) L319P probably damaging Het
Nelfa A G 5: 34,056,620 (GRCm39) probably null Het
Or5b97 A C 19: 12,878,803 (GRCm39) Y114D probably damaging Het
Pcdha11 T A 18: 37,138,870 (GRCm39) N166K probably damaging Het
Pcdha6 C A 18: 37,102,269 (GRCm39) N487K probably damaging Het
Pcsk2 A G 2: 143,415,460 (GRCm39) D91G possibly damaging Het
Pigp A G 16: 94,171,065 (GRCm39) F22L probably benign Het
Pnpla8 A C 12: 44,329,670 (GRCm39) N74T probably benign Het
Ppargc1b T C 18: 61,448,980 (GRCm39) K114R probably damaging Het
Ppfia2 A G 10: 106,693,430 (GRCm39) D645G probably damaging Het
Rnf213 G A 11: 119,332,854 (GRCm39) V2688I probably benign Het
Rnf43 A G 11: 87,622,951 (GRCm39) H557R probably damaging Het
Rp1l1 C T 14: 64,267,545 (GRCm39) P1044S probably damaging Het
Rrp9 G A 9: 106,360,221 (GRCm39) D210N probably damaging Het
Scin G T 12: 40,129,807 (GRCm39) Q329K possibly damaging Het
Scn7a T A 2: 66,534,244 (GRCm39) H477L probably benign Het
Slc26a8 A T 17: 28,888,914 (GRCm39) M195K probably benign Het
Spata13 A G 14: 60,993,877 (GRCm39) K1110E probably damaging Het
Spata24 T A 18: 35,793,503 (GRCm39) E103V probably damaging Het
Srek1 T C 13: 103,910,894 (GRCm39) N25S probably damaging Het
Strada T C 11: 106,064,140 (GRCm39) Y59C probably damaging Het
Tnrc6c T C 11: 117,626,831 (GRCm39) W1143R probably damaging Het
Trip12 A T 1: 84,738,559 (GRCm39) D765E probably benign Het
Ttbk2 G A 2: 120,580,798 (GRCm39) R444C probably damaging Het
Ush2a T A 1: 188,644,303 (GRCm39) I4555N possibly damaging Het
Vcan C T 13: 89,838,045 (GRCm39) E2500K probably benign Het
Wdfy4 T A 14: 32,693,668 (GRCm39) H2719L probably damaging Het
Zfhx2 T C 14: 55,311,653 (GRCm39) D347G possibly damaging Het
Zfp653 G A 9: 21,969,558 (GRCm39) T236I probably damaging Het
Zscan4-ps1 A T 7: 10,799,913 (GRCm39) H325Q probably benign Het
Other mutations in Vps16
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01327:Vps16 APN 2 130,279,616 (GRCm39) missense probably benign 0.19
IGL01400:Vps16 APN 2 130,280,273 (GRCm39) missense possibly damaging 0.73
IGL01542:Vps16 APN 2 130,280,314 (GRCm39) missense probably damaging 0.97
IGL02011:Vps16 APN 2 130,283,399 (GRCm39) missense probably benign 0.04
IGL02192:Vps16 APN 2 130,282,852 (GRCm39) missense probably damaging 0.98
IGL02220:Vps16 APN 2 130,283,573 (GRCm39) missense possibly damaging 0.85
IGL02587:Vps16 APN 2 130,281,636 (GRCm39) critical splice donor site probably null
R0427:Vps16 UTSW 2 130,280,770 (GRCm39) missense probably benign 0.00
R0507:Vps16 UTSW 2 130,279,632 (GRCm39) critical splice donor site probably null
R1550:Vps16 UTSW 2 130,282,260 (GRCm39) missense probably benign 0.09
R1789:Vps16 UTSW 2 130,285,520 (GRCm39) missense probably benign 0.42
R3895:Vps16 UTSW 2 130,280,596 (GRCm39) missense possibly damaging 0.96
R3981:Vps16 UTSW 2 130,284,514 (GRCm39) missense possibly damaging 0.77
R4092:Vps16 UTSW 2 130,281,832 (GRCm39) missense probably damaging 1.00
R4555:Vps16 UTSW 2 130,285,496 (GRCm39) missense probably damaging 1.00
R4569:Vps16 UTSW 2 130,284,124 (GRCm39) missense probably benign
R4803:Vps16 UTSW 2 130,280,030 (GRCm39) missense probably benign 0.27
R4835:Vps16 UTSW 2 130,280,220 (GRCm39) splice site probably benign
R5022:Vps16 UTSW 2 130,281,372 (GRCm39) missense probably benign 0.07
R5023:Vps16 UTSW 2 130,281,372 (GRCm39) missense probably benign 0.07
R5057:Vps16 UTSW 2 130,281,372 (GRCm39) missense probably benign 0.07
R5158:Vps16 UTSW 2 130,283,199 (GRCm39) missense probably damaging 1.00
R5177:Vps16 UTSW 2 130,285,288 (GRCm39) nonsense probably null
R5540:Vps16 UTSW 2 130,284,305 (GRCm39) missense probably benign 0.00
R5680:Vps16 UTSW 2 130,282,244 (GRCm39) missense possibly damaging 0.64
R5689:Vps16 UTSW 2 130,281,011 (GRCm39) nonsense probably null
R5690:Vps16 UTSW 2 130,281,011 (GRCm39) nonsense probably null
R5926:Vps16 UTSW 2 130,285,476 (GRCm39) missense probably damaging 0.97
R5992:Vps16 UTSW 2 130,266,369 (GRCm39) critical splice donor site probably null
R6370:Vps16 UTSW 2 130,285,304 (GRCm39) missense probably damaging 1.00
R6898:Vps16 UTSW 2 130,279,601 (GRCm39) missense possibly damaging 0.74
R7378:Vps16 UTSW 2 130,280,099 (GRCm39) missense probably damaging 1.00
R7487:Vps16 UTSW 2 130,280,977 (GRCm39) nonsense probably null
R7641:Vps16 UTSW 2 130,282,448 (GRCm39) missense probably benign 0.28
R7720:Vps16 UTSW 2 130,283,623 (GRCm39) nonsense probably null
R8246:Vps16 UTSW 2 130,280,793 (GRCm39) missense probably damaging 1.00
R8363:Vps16 UTSW 2 130,284,161 (GRCm39) missense probably benign 0.08
R9092:Vps16 UTSW 2 130,281,593 (GRCm39) missense probably damaging 0.99
R9128:Vps16 UTSW 2 130,266,319 (GRCm39) missense possibly damaging 0.51
R9352:Vps16 UTSW 2 130,283,823 (GRCm39) critical splice donor site probably null
R9406:Vps16 UTSW 2 130,283,425 (GRCm39) critical splice donor site probably null
R9508:Vps16 UTSW 2 130,284,361 (GRCm39) missense possibly damaging 0.94
R9800:Vps16 UTSW 2 130,282,405 (GRCm39) missense probably benign 0.02
RF021:Vps16 UTSW 2 130,280,129 (GRCm39) missense probably benign 0.09
Z1177:Vps16 UTSW 2 130,283,346 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CACGGATATGCTTCCAGACTG -3'
(R):5'- CATCCAGATGTAGCCTGTGTC -3'

Sequencing Primer
(F):5'- CTGGAACCAGCAGAGACAC -3'
(R):5'- TACGTGAAGGATACAGCCATCTG -3'
Posted On 2017-10-10